As it Should Be
by Beastial Moon
Summary: Skipper's life after the adventures. He knows something is wrong in the back of his mind. Will he find out what? Mostly OC's.
1. Chapter 1

**This is the Final Installment in my series. Lots of OC's, and 100% AU/AT, whatever you want to call it. First chapter is a GO!**

Skipper walked down the muddy embankment. The work was hard, and long. His only reason for going on was the competitive urge deep within. He was 18.

He was working for the Navy. He was not yet in it, but he was training. Training to be the Best. Skipper knew he could be "The Best" because…. Well, just because. His white feathers were blackened by the mud and grit. He trudged on, hiking. Hiking, all they ever did was hike. Hike, Hike, Hike, shoot, target practice, and real-life scenarios. What could go wrong would go wrong. That was the motto of the sergeant.

There were five altogether in the posse of militant soldiers.

Jack, the egomaniac penguin leader.

Susannah, the white penguin who was part albino. She did not have red eyes, but her feathers were all white. It came in handy when hiding from enemies in the snow, but not much else.

Cole, the new penguin. He was British, but he was very adorable. Something about him gave Skipper the creeps, but he wasn't sure what.

Doris, a dolphin from off the coast of America. She mostly kept to herself, and helped when they could.

The last one was Skipper.

The hike was nearly over. They could see base camp ahead of them. The team was so tired now that they could barely make it down the hill without tripping.

Once in the Base Camp, Sergeant greeted them. "You did well today, men. Take the afternoon off." The team immediately went to their bunks. They were concrete, with a small mattress over top and a pillow. The mattress was not small to the penguins, but it would be to a human.

Skipper thought about the next day. They would be simulating with older soldiers. They would have to do something. They wouldn't say what, which was just fine with skipper. He liked to be surprised. He was ready for anything. He was assigned to a penguin with a strange name – Rico. The very thought of him made his blood run cold. He sounded menacing. Why was he so scared of a Name? He didn't know, and didn't care. He slept.

**This was just a quick chapter to introduce some of the characters. Tell me what you think, mainly by reviewing.**


	2. Chapter 2

As it should be

Chapter two

I apologize for the long wait between chapters. The first chapter was different than what I had originally planned, so I had to make some changes. On top of that, I got sidetracked. I am working on four different stories at once. Not fun.

Special kudos to none of your business, that review really snapped my attention back to the story.

And, here we go.

Six Years Later

"Men, move out!" Skipper called. Rico guarded Skipper's back. Space squids were all around them. Skipper's men fired shots, and threw knives at the squids. They inflicted little damage, only bruises and a few cut ends.

A large squid slithered to the penguins. "Sai Skipper."

"Sai Morten." Skipper fell into a defensive position. He glared distastefully, locked in battle mode. Rico regurgitated a time bomb – the regurgitating a thing he had learned long ago in his training. It flew into the air, landing at the tentacles of the space squid.

Two tentacles erupted from Morten. The one knocked the bomb out of the way, exploding harmlessly into the ice wall. With the other, he clutched Skipper around the shoulder/waist. He brought Skipper closer, tentacle toiling, suckers sucking.

"Now, Skipper – will you surrender?" half of skipper's men were dead, the remaining wounded. Rico had a shotgun cocked at his head.

"Your friends are dead, you have lost. Will you surrender?" Skipper stayed silent. He would not, nor would he give them the chance to. Before he could act out his plan –

"Kill him" came from Morten's beak. A shot rang out. Some miraculous way, it missed Rico. But Skipper didn't know. All he could see was blood. It was all he could smell. A blind fury came over him, literally taking away his sight. He let it take over, subsiding to rest in a dark corner of his mind.

"Skipper- Skipper, stop. Stop, Skipper. STOP!" he heard voices. Voices he knew. Rico. Morten. The test.

It was all a test.

He calmed himself. "I'm sorry, Morten." he hung his head.

"Nonsense, lad. You showed a duty to protect your brethren, in life and in honor. You did good. I will have to talk with the Elders, but I think this may be your year." Skipper smiled. The squids slid out of the room, leaving the penguins to take care of themselves. None of them actually died, of course. It was all a show. If the team passed, they were sent into the field. Skipper and his team had been going for a few years now. Three, exactly.

Skipper turned to Rico. "I think we passed" he said. Rico nodded. For some reason, he found it easier to talk with actions and less with words. Just a feeling.

"I certainly hope so."

The next Day

Skipper adjusted his tie. The bowtie made him itch. It was blue, to match his eyes. He looked at his bunk partner.

Rico had a grin on his face. He was one of the oldest on the force, if he didn't make it this year, he had only one more year and that was it. He had faith that this was his year.

They walked down the hall to the auditorium/ conference room. Together, they found a pair of seats – close to the aisle, yet strategically around the middle. They sat down.

The curtains were drawn. Seven panels for seven judges. They stood behind each panel, waiting to read off the names.

The Director stood behind the podium to the right of stage.

"I'd like to begin with a few starting words…" she began. Within minutes, Rico and Skipper were both asleep.

It droned on for hours. The Director would call a name. that penguin, or whatever animal they were, would come down on stage, shake all of the judges hands, proceed across the podium with a stern salute, and walk off.

Around the O names, Rico woke Skipper. The two were overly anxious to hear their names called.

"Quentin – Qubert – Raymond – Ricardo – Roland –"Skipper hung his head. Rico looked to the sky, thinking "why?"

Skipper patted his friends back in comfort. "There's always next year" he said. Rico sniffed.

On the other hand, since he wasn't called, that means that Skipper did not pass either.

"Skipper." oh. Apparently I was wrong, he thought. Skipper could do nothing, but shake his friends hand and walk downstage.

Once off stage, he was told to follow a group of other animals. He told them he had to wait to see who made it to the Special Ops mission, at least. They let him stay.

The Special Ops were a covert force, so secret only the seven Elders knew what went on. The Director babbled on about how special it was to be accepted into this Secret Agency. Finally, he read off the names.

"Maximillian, Rico, and Zacharius." skipper looked at his friend. His mouth was hanging open. He stood up and shut his mouth, walking down the aisle to the stage. The three of them went to the left, near the Elders, instead of Right like the others. Skipper smiled. Rico deserved this.

He watched Rico walk away to his new life. After a bit, Skipper turned around and walked to his. He followed a group of Penguins down. Everybody was given a card, with the airplane number they were supposed to have. Skipper glanced a look at his card. F-B2. He followed down the F hangar.

A hum went on. Thinking it was his plane lifting off, he ran towards the plane. Around the corner came a female otter. They ran into each other, cards falling to the ground.

"I'm so sorry, I am in so much of a hurry." she apologized. She picked up the Card closest to Skipper and handed it to him as he dusted himself off.

"No, no, I'm fine, miss…?"

"Marlene. My name is Marlene."

"Ah. Well, I'll be on my way."

"Yeah.. Bye." She ran away.

Skipper looked back at his card. F-B4. It didn't seem right. He shrugged, and got on the plane.

There were seven seats in the plane. Four were taken; he was the last one to enter, as the door shut behind him. No backing out now. He strapped himself into the seat, in between two of the animals. All his partners were female.

Doris was there, that was a nice surprise. She seemed surprised as well that he was here. "I'm skipper." he announced. The penguin to his right ignored him. The one to his left said hi. "I'm Guinevere. Everyone calls my Gwen." she held out a flipper. He shook it.

The pilot walked in. "We're in the air, now. I will quickly debrief you on your mission. You are to stake out a force in NYC. From there, you will remain incognito while The Special Ops do their job. Once you get word from them, they'll tell you what to do."

"It may take a while for them to get to you, seeing as you are Option G. Good luck." He returned to the cockpit.

They proceeded greeting each other. The snow hare in front of Skipper said

"Hi, my name's Susannah. You can call me Sue."

Everyone looked at the female pengun. She didn't even bother looking up from her notes. "My name is Sokka. Don't misuses it, don't forget it. End of story."

She'd like Rico. Skipper thought.

**Well? How'd I do? I'm a little rusty on the story, so let me know how I'm doing so far.**


	3. Chapter 3

**As it should be **

**Chapter 3**

**I apologize for the long wait between chapters. I was going to go one direction with the story, but I switched it around a bit and now I'm having a bit trouble. I'm good now though, so it should be up in a speedier fashion. On with the story!**

Skipper looked over the files. It had been months into their operation. Their base was in the Central Park Zoo. When they had come into their habitats, the penguins (Sokka and Skipper) found the base already set up. It all looked familiar to him somehow. The strong sense of déjà vu was overpowering. He had gotten dizzy the first time he entered the HQ. He still got a little dizzy every time he was in there, so he spent as much time as he could up top.

Not much was happening. they had to wait for orders from the team up. So for now, they posed as zoo animals.

That night….

He went into Doris's habitat. She held a picture, staring sadly. When she noticed Skipper, she quickly tried to hide it.

"What was that?" Skipper asked. She slowly pulled the picture back out. It was a picture of the Otter Marlene and Doris. On the back was a note labeled "friends 4ev" 2010.

skipper gave it back to her. "How'd you get that?: he asked

"My parents told me it floated by a few minutes after I was born. It's strange… three years after they found this, I met the creature Marlene. She's been my best friend. She was supposed to come with us on this mission, but she never came." Skipper gulped

"Did she remember taking the picture?" he asked

"No. I asked her. And I don't either." she replied coolly.

"Well, I'm sure she's fine. Wherever she is." Skipper comforted.

"Yeah." she put the picture away. Not sure what else to do, Skipper got up and left.

The following notes were taken from the Skipper's Log, 1991.

March 31st. New arrival. His name is Kowalski. He passed the psyche screening with flying colors. Maybe too fly. I'm suspicious. He's smart. I'm keeping an eye on him to make sure he's not a spy. Training commences in the A.M. I plan to see what he can do.

April 1st. Kowalski did good on his training – but it could be better. He's very handy with a clipboard and thinking. I think he'll be my options penguin. On another note, the team wants me to be team leader. I declined such a position. I'm having doubts though. Something about being leader appeals to me, but I have no idea what.

April 3rd. Susannah started doing everything I told her today. This is no more than normal, but still. She seemed – nicer, somehow. Especially around me. Something's up, and I plan on finding out what.

I keep getting flashes. Memory flashes, memories I haven't had (or had yet). Something's wrong with me. I walk around each day in a haze, barely focusing on anything around me. It's like a migraine of Déjà vu.

I'm scared of what I am.

April 15th. Kowalski was working on his next invention. It was a Time Cabinet, as he called it. He said with this device they could go anywhere in time that they wanted to. He said that the space-time continuum had a sort of knot in it, and he had to fix that first. On a related note, he keeps trying to show off around Doris. I think he has a crush on her.

speaking of Crushes, Susannah told me shocking information. She likes me. I'm not sure I like her back, though. Something stops me, but I don't know what. I hate lacking information.

April 17th.

The team up from us asked for a profile on the human race. Anatomy, emotions, reasoning, psychology. It took a while, but we got it done. It sits on the table in front of me now. I told Sue I wasn't interest in a relationship, and now she's mad at me. I'm going to stary holed up here until things get better. Kowalski's in charge of the Recon tonight.

End Log

In a Separate place (April 18th)…

Rico sputtered on the sidewalk. He had to get to skipper. Trouble was brewing back at the main Headquarters. Central Park Zoo was only a few blocks away. If he had made it this far, he could make it further. He needed Skipper's help. But how could he tell Skipper what was going on when he couldn't speak?

End Chapter


	4. Chapter 4

**As It Should be chapter 4**

**See, I told you I'd get the next chapter up quick! How could you doubt me? Anyway, there's only a few chapters left. So enjoy it while you can!**

Skipper sipped his coffee. He looked off to the gates. There was something in the distance. It looked like a penguin. He grabbed his binoculars. It was Rico! He was in trouble! Hurriedly, he called Guinevere on a Walkie Talkie.

"There's a hurt penguin at the front gate. See if you can bring him in. Doris, are you there?"

"Yeah"

"Okay, I'm going to need your medical expertise on this."

"On it, Skipper." In seconds, Guinevere and Doris were working on Rico on the floor of the concrete ice floe. Doris assessed the damage.

"Fractured leg… bruises and cuts along his back and stomach… well, this is odd."

"What? What is it?" Skipper asked.

"His gullet seems to be made of steel." She thumped Rico's stomach, metal ringing out. "And His voice box is almost completely ripped out." Skipper kneeled closer. He could see it too. It was odd. There seemed to be – a sort of tunnel in his throat. He and Doris shared a glance. What was the military doing?

They moved him to one of the far bunks below the habitat. When he finally came around, he muttered.

"What was that, Rico?" Doris asked "gagidbllllr!" He attempted to respond. He knew he couldn't, but it was worth a shot.

"Oh, I'm sorry. I forgot to tell you, your voice box is almost completely ripped out. You can't speak, and there is an extremely low chance of ever talking again." Rico hacked up a post it box and pencil, writing speedily. Kowalski saw this, and rushed over from his work table.

"Tell me something I don't know" Rico wrote

"How Did You Do That?" Kowalski asked excitedly.

"The secret place I work – is Dallas. Dallas Texas. In the Hoover Building." he wrote fast in an attempt to get it all down at once. "I was a test subject. All three of us were test subjects! There is no 'Special Ops', it's a lie to make recruits excited to join."

"And you fell for it." Doris finished

"Exactly. My stomach was given an arsenal of weapons, which I hack up through a special valve in my throat – where my voice box was." Rico looked up to Kowalski. "Do I know you?" he wrote

"N-no. Not that I am aware."

"Oh." and he fell back asleep.

Skipper was topside during the whole conversation, so Doris and Kowalski had to tell him what happened.

"Odd." Skipper muttered. "What?" Kowalski asked

"Well, I thought he looked familiar when I first met him, all those years ago. The same went for you. Now he thinks he knew you? I don't think these bouts of déjà vu are a coincidence."

Kowalski flipped through his notes. "Skipper, you know how I've been working on traveling through the space time continuum?"

"Yesss…" "Well, it all seems to be focusing itself on this habitat."

"No!"

"Yes! And to pinpoint it even further, the Time-Knot (my name, I copyrighted it) comes down to – you. You are a paradox, a rip in space-time!"

Skipper fainted.

Skipper woke up in his bunk. "W-what's going on?" he asked.

"Ah, you're awake. You fainted. We dragged you in here, put you in your bunk. Meanwhile I fixed up the Time Cabinet and found something – well, strange."

"How strange?"

"You'll have to see for yourself. It's on the computer." Kowalski pulled his laptop out of nowhere, and began to show skipper pages.

"This human child has portrayed your entire life's story through the pages of this website. It's called /Penguins of Madagascar."

"And what is the boy's name?"

"I cannot find his actual name. His username is Beastialmoon."

**How's that for a cliff hanger? No, this is not going to be another Gary Stu. I'm not even entirely sure what those are. You'll have to wait to see what I am up to. Muahahahahaha!**


	5. Chapter 5

As it should be chapter five

Wow! I am updating these extremely fast! Something must not be right with me! jk. Here's the next chap. And before I forget, Review!

"What, exactly, are the stories about?" Skipper asked

"Well, so far there's been a trilogy of stories. The last chapter of the third one was updated in July. In the first it is set in what seems to be the 'normal' (quote/unquote) Penguins of Madagascar world. The next one gets a bit weird."

Skipper read the story with intense satisfaction. The words on the page – they were real. Everything happened, he could feel it. But how was this possible?

"Wait – so my whole life has been determined by some geek on his computer?" Skipper was freaking out. "So not only am I a rip in the Space-Time continuum, I also have my every move planned out by some – human!"

"Relax, Skipper. It's not quite that bad."

"Oh? Tell me why!"

"He hasn't finished his third story. You've lived most of your life in free will. I have also messaged the human so you can ask him whatever."

"I – I need to think." Skipper headed into the hidden car/invention hold. Kowalski shook his head in pity. Kowalski went back to work. Sokka worked on making sure Rico was alright.

Sokka looked at his closed lids. He was beautiful… even with the scar and inability to speak. The scar made him appear that much sexier. She stroked his face. Rico's flipper went up, grabbing it. She let out a tiny gasp.

"Wh- what?" he murmured. His eyes were still closed. "Shhhhh. don't be afraid." she whispered in his ear, beak going closer to his lips. They kissed. At the end of it Rico opened his eyes.

"Wow." he muttered. It was the most he could say, and even that sounded guttural. Sokka giggled. He was funny, too. Not like the other jerks back at the training base.

Skipper came back in the room. "Kowalski, I've made my decision. What can I do to – whoa!" skipper and Kowalski just noticed Sokka and Rico snogging.

"What in blue blazes is going on?" he exclaimed

"Well, I, um – you see, he… "Sokka stammered. Rico interrupted by wolf whistling.

"Oh, is that all? Hmmph." Skipper didn't complain. "Well, enjoy it while you can." Everybody looked at him.

"In a few days, I will be leaving you – forever."

"No! Why are you leaving us!" Rico wrote. Kowalski explained Skipper's situation. A ding was heard from the laptop. Kowalski, Skipper, Rico and Sokka walked over to it. There was a message from Beastialmoon. It read;

"Hello. My name is Beastialmoon, I do not feel like giving away my name right now. What kind of questions do you wish to ask?"

Kowalski opened up a reply. "Alright, Skipper. He's all yours." Skipper began typing.

"My name is Skipper. I have read your stories, and they seem to have an uncanny similarity with my life. How did you manage to do so? Please tell me everything." he clicked send.

A few seconds later, the reply came.

"Holy sh! %! Sorry for my language, but, just – whoa! I was just writing what I thought was a fictional story! I never imagined it would be real!"

Skipper typed back, "Thanks. I feel so much better knowing my life is fiction."

"That's not what I mean. Look at it this way. Words have more power than any of us can deal with. What writing really is, is magic. I can write a story, and someone can read it weeks, months or even years down the road and see the same thing as me in the story. It travels across time and space. I have taken this idea from a book I read, so if you know it don't yell copyright. All rights to Stephen King."

"Who? And what does this have to do with anything?"

"Never mind. I think something happened in your time travel that may have awakened the idea within me, or maybe it is just fiction and it coincidentally is viewed from a parallel world. We may not even be in the same universe!"

"What can I do?"

"I haven't gotten that far. I was going to have you travel to the Dark Tower, but that seemed to cliché. I had writer's block."

"Well, thanks for your help. Bye." Kowalski turned off the screen.

"That's a lot to take in." Rico wrote. "Yeah." Sokka agreed.

"And you know what? The story's not finished yet. Kowalski."

"Yes, Skipper?"

"Why are you still standing here! Get to work on that Time Cabinet!"

Not much of a cliff hanger, but still. Only one or two chaps and then its over. Again, I apologize for the long delay with the first three chapters. REVIEW!


	6. The Final Chapter

**As It Should Be: The Final Chapter**

**Here it is, folks. I finally have the final chapter of the trilogy posted. I hope you like it, and find the insatiable urge to review. So give in to that urge, and review when you are done reading!**

Kowalski kept at work on his Time Cabinet. The days went by, Kowalski working overload. Rico and Sokka grew closer together. Pretty soon, they weren't seen apart. Their flippers were glued to each other. Guinevere helped Kowalski out when possible, and Doris and Skipper kept up their surveillance operation.

One morning…

Only Sokka and Kowalski are in the room. Kowalski looked over his notes, and the cabinet. Carefully checking every function. He opened the door. Light burst from it, then quickly subsiding. Behind the door was another world – paradise. A world where nothing was perfect, but they all got along in their own little way. Sokka was mesmerized in this world.

Hypnotized, almost. She started walking towards it, the trio of strange monkey creatures and the penguins in that other zoo. Rico was there! His scar was a little different, but mainly the same personality. She reached out…

…And almost got her hand slammed in the door. "Sorry, Sokka. But I don't know if it will work on any other creature than Skipper." Kowalski apologized. "Can you get the others for me?"

She hesitated, still under the new world's spell. Then she nodded her head, and slowly went up top.

"Skipper." she called. Skipper looked up from his map of the zoo, and everyone looked at Sokka.

"It's time."

Skipper stood up, and walked over silently. Everyone was quiet with a solemn grace. When everyone piled into the Penguin's room, it was so crowded it was hard to move. But everyone managed to get to see Skipper and the Time Cabinet.

"Gentlemen and ladies, I am about to go on an epic quest… a quest to find the truth about my past. I don't know if I will return, or if it is possible for me to return. I wish you all the best in all you do. Kowalski, you are Colonel now. Take care of the Troops." Kowalski moved a tear from his eye.

"Kowalski, are you crying?" Doris asked.

"No, it's just very dusty in here." he said "I'm having an eye reaction."

Skipper looked back at them. Doris and Guinevere in the back, looking over everyone. Sokka and Rico side by side, gripping each other with passion. Kowalski at the Time cabinet. Kowalski pulled goggles over his eyes. He pressed a few buttons on the side of the cabinet. Skipper opened the door. the light burst out again, tearing their eyes. It flowed back in, like a magnet. Skipper started across the threshold.

He disappeared into the new world. They saw him one minute, the next he was talking to the three penguins on the ice floe, calmly. Someone screamed.

They were disappearing. Something wrong was happening, very wrong. Sokka could feel her essence slipping away. She struggled to the Cabinet. Rico reached out for her. "Grokkergh!" He managed to get out.

She looked back to him as she leaned against the Cabinet. "I'm sorry, Rico. I love you." and she stepped across.

It was like being pulled in every direction. All her senses disappeared, then returning with a WHUMP.

She opened her eyes. She was standing with the other penguins. All four were looking at her strangely. "Who are you?" skipper commanded. "Skipper, it's me. Sokka. Don't you remember?"

"I've never seen you before in my life." he replied coldly. Sokka's heart filled with dread. This was wrong, so very wrong. Then again, maybe this was the way it was supposed to be. She sighed.

"In another life, you did." She pecked Rico on the cheek, and went down into the HQ. Rico just stood there, stunned.

"Who was that strange female penguin, Kowalski?" Skipper asked.

"I do not know."

"Well, for the meantime, add her into the roster."  
"Aye, Skipper."

Weeks go by. Sokka tried to go out with Rico. He was the same as the other Rico.

And yet, not the same. He didn't have as much of a sensitive side as the other one. She cried in her sleep. She realized what she was, but never told anyone.

She was homesick. She recorded a message on skipper's blank tapes, and labeled them off to Private. He would keep them secret until the time was right. Inside was everything Skipper would need to know… when the time was right.

It was night now. She got out of bed, being sure not to wake anyone. She snuck the tapes under Private's pillow. Giving Rico another quick kiss on the lips, she went up the ladder.

The sun shone the next morning. Rico held his flipper over his eyes. What was sunlight doing in the HQ? He looked up. Sokka was gone, and the fishbowl entrance was left open. Luckily, he was the first one up. He quickly shut the entrance. Then the alarm sounded, and they got into their stances. A new day, another adventure.

Everything was back to normal… as normal as The Penguins of Madagascar was going to get.

For now.

**That is the end! Thank you for reading the story, I hope you liked it as much as I did! I sort of made a sequel, its set after this story. It's called "Skipper and the Church of Destiny." Nothing in it relates to this trilogy, but the sequel to that one ("The Unforgiven Trilogy") has much to do with it. So enjoy, and review!**


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